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- PDB-8jee: Crystal Structure of Human Carbonic Anhydrase II In-complex with ... -

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Basic information

Entry
Database: PDB / ID: 8jee
TitleCrystal Structure of Human Carbonic Anhydrase II In-complex with Levosulpiride at 2.96 A Resolution
ComponentsCarbonic anhydrase 2
KeywordsLYASE / Human Carbonic Anhydrase II / Levosulpiride
Function / homology
Function and homology information


positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / morphogenesis of an epithelium / regulation of intracellular pH / carbonic anhydrase / carbonate dehydratase activity / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / neuron cellular homeostasis / one-carbon metabolic process / apical part of cell / myelin sheath / zinc ion binding / extracellular exosome / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Carbonic anhydrase, alpha-class, conserved site / Alpha-carbonic anhydrases signature. / Carbonic anhydrase, alpha-class / Alpha carbonic anhydrase domain / Alpha carbonic anhydrase domain superfamily / Eukaryotic-type carbonic anhydrase / Alpha-carbonic anhydrases profile. / Eukaryotic-type carbonic anhydrase
Similarity search - Domain/homology
: / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.96 Å
AuthorsRasheed, S. / Huda, N. / Falke, S. / Fisher, S.Z. / Ahmad, M.S.
Funding support Pakistan, 1items
OrganizationGrant numberCountry
Not fundedRef No. 20-17595/NRPU/R&D/HEC/2021 2021 Pakistan
CitationJournal: To Be Published
Title: Crystal Structure of Human Carbonic Anhydrase II In-complex with Levosulpiride at 2.96 A Resolution
Authors: Rasheed, S. / Huda, N. / Ahmad, M.S.
History
DepositionMay 15, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6246
Polymers28,9331
Non-polymers6915
Water81145
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.323, 41.774, 71.729
Angle α, β, γ (deg.)90.00, 104.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Carbonic anhydrase 2 / Carbonate dehydratase II / Carbonic anhydrase C / CAC / Carbonic anhydrase II / CA-II / Cyanamide ...Carbonate dehydratase II / Carbonic anhydrase C / CAC / Carbonic anhydrase II / CA-II / Cyanamide hydratase CA2


Mass: 28932.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Escherichia coli (E. coli)
References: UniProt: P00918, carbonic anhydrase, cyanamide hydratase

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Non-polymers , 5 types, 50 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-U6X / Levosulpiride / ~{N}-[[(2~{S})-1-ethylpyrrolidin-2-yl]methyl]-2-methoxy-5-sulfamoyl-benzamide


Mass: 341.426 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N3O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: Crystallization solution was comprised of Tris-HCl buffer (50 mM, pH=7.4), and 2.9 M ammonium sulfate. Crystallization drop was comprised of hCA-II, Acetohexamide and reservoir buffer.
PH range: 7-8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.5406 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Feb 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 2.96→19.96 Å / Num. obs: 5191 / % possible obs: 99.6 % / Redundancy: 3.3 % / CC1/2: 0.74 / Rrim(I) all: 0.411 / Net I/σ(I): 18.2
Reflection shellResolution: 2.96→3.14 Å / Num. unique obs: 819 / CC1/2: 0.707 / Rrim(I) all: 0.524

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Processing

Software
NameVersionClassification
PHENIX(1.18_3861: ???)refinement
PROTEUM PLUSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KS3

3ks3


Resolution: 2.96→19.95 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2482 254 4.9 %RANDOM
Rwork0.2176 ---
obs0.2191 5181 99.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.96→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 40 45 2134
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012147
X-RAY DIFFRACTIONf_angle_d1.2932915
X-RAY DIFFRACTIONf_dihedral_angle_d15.994788
X-RAY DIFFRACTIONf_chiral_restr0.074302
X-RAY DIFFRACTIONf_plane_restr0.007374
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.96-3.730.26511370.24282424X-RAY DIFFRACTION100
3.73-19.950.23041170.1962503X-RAY DIFFRACTION100

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